[English] 日本語
Yorodumi
- PDB-5di5: beta1 t801 loop variant in P3221 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5di5
Titlebeta1 t801 loop variant in P3221
Componentsbeta1 t801 loop variant
KeywordsDE NOVO PROTEIN / synthetic protein / protein design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsMacDonald, J.T. / Kabasakal, B.V. / Murray, J.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension.
Authors: MacDonald, J.T. / Kabasakal, B.V. / Godding, D. / Kraatz, S. / Henderson, L. / Barber, J. / Freemont, P.S. / Murray, J.W.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: beta1 t801 loop variant


Theoretical massNumber of molelcules
Total (without water)25,4801
Polymers25,4801
Non-polymers00
Water34219
1
A: beta1 t801 loop variant

A: beta1 t801 loop variant


Theoretical massNumber of molelcules
Total (without water)50,9602
Polymers50,9602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area1370 Å2
ΔGint-15 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.460, 123.460, 47.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein beta1 t801 loop variant


Mass: 25479.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pRSETA-thr / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.22 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10mg /ml protein solution mixed with equal volume of 0.2 M ammonium acetate, 0.1 M Bis Tris pH 5.5, 45% v/v MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.28→106.92 Å / Num. all: 19284 / Num. obs: 19284 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 15.3
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.449 / Mean I/σ(I) obs: 1.8 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: theoretical protein model

Resolution: 2.28→53.46 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1875 919 4.77 %random
Rwork0.178 ---
obs0.1784 19259 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→53.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 0 19 1389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071380
X-RAY DIFFRACTIONf_angle_d1.4081878
X-RAY DIFFRACTIONf_dihedral_angle_d15.876480
X-RAY DIFFRACTIONf_chiral_restr0.059223
X-RAY DIFFRACTIONf_plane_restr0.009261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2801-2.40030.32451470.26582557X-RAY DIFFRACTION99
2.4003-2.55060.26051360.24672562X-RAY DIFFRACTION99
2.5506-2.74760.2391060.22552609X-RAY DIFFRACTION99
2.7476-3.02410.20891230.19532626X-RAY DIFFRACTION100
3.0241-3.46160.2341360.18792610X-RAY DIFFRACTION100
3.4616-4.36090.14231320.14362653X-RAY DIFFRACTION100
4.3609-53.47440.16141390.16522723X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.0675-1.53943.18514.40810.27591.86540.44210.83531.0558-1.32450.2719-0.0205-0.0836-0.3213-0.72180.8266-0.06880.00680.66340.13150.587562.6265-18.9633-26.9891
24.48790.99211.27824.5763-1.65839.4241-0.18370.29150.0156-0.01660.2333-0.1472-0.6210.1652-0.05870.3612-0.06690.04380.37370.02020.404661.8205-19.8733-17.5711
35.7807-2.52024.76463.5673-3.48134.6921-0.00790.4853-0.0287-0.1499-0.04530.01910.0410.73320.03050.4577-0.00090.04220.46420.0310.446263.3961-27.7322-19.5309
43.9099-0.3351-0.06895.21350.98166.80050.09560.05610.1324-0.31760.02560.0344-0.4828-0.0655-0.07950.41520.00310.01350.38230.00940.40256.6904-24.094-15.7784
52.51311.05380.17373.30140.9045.7951-0.074-0.02980.36030.1031-0.01520.1996-0.3344-0.0310.10130.37860.05380.01290.41140.01540.463452.3134-26.7038-13.748
66.7365-0.88931.99743.2981-0.92057.1524-0.0814-0.19760.33540.034-0.01540.3307-0.5356-0.32130.01540.38690.03620.02510.42480.01520.447246.1569-27.5718-14.1795
72.36610.1733-0.89233.35751.91214.1665-0.03880.1603-0.0510.0264-0.03260.2137-0.0201-0.35790.08420.41180.01380.01470.51010.04460.487242.6513-34.849-12.1605
83.1879-5.51091.82259.842-1.65196.13160.3106-0.5203-0.26190.33150.16360.4553-0.1314-0.4067-0.30710.4078-0.10220.03860.54530.04460.46839.7717-35.376-7.3857
92.3531-0.1931-0.14483.09210.1913.02310.3638-0.4103-0.1136-0.0751-0.22580.23280.0378-0.7029-0.10220.3513-0.08850.0440.60260.04080.457835.4168-40.5345-10.5676
106.8934-0.7609-2.08444.8801-0.47014.97390.24980.32940.17020.0025-0.0969-0.2136-0.0868-0.19990.01240.4574-0.1428-0.03870.64990.040.523231.229-48.3706-6.3234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 49:55)
2X-RAY DIFFRACTION2(chain A and resseq 56:73)
3X-RAY DIFFRACTION3(chain A and resseq 74:81)
4X-RAY DIFFRACTION4(chain A and resseq 82:103)
5X-RAY DIFFRACTION5(chain A and resseq 104:128)
6X-RAY DIFFRACTION6(chain A and resseq 129:164)
7X-RAY DIFFRACTION7(chain A and resseq 165:186)
8X-RAY DIFFRACTION8(chain A and resseq 187:199)
9X-RAY DIFFRACTION9(chain A and resseq 200:223)
10X-RAY DIFFRACTION10(chain A and resseq 224:241)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more